MutationT@ster 2025

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Input seems to be ok - now mapping the variant to the different transcripts...
Querying Taster for transcript #1: ENST00000325006
Querying Taster for transcript #2: ENST00000446544
MT speed 0.13 s - this script 2.567709 s

Transcript summary:

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Transcript	Gene symbol	Prediction	Tree vote	Model	Prediction problem	Splice site change	Known ClinVar disease mutation	Potential ClinVar disease mutation	Amino acid changes	Variant type	dbSNP ID	Protein length	Features at a glance
ENST00000325006(MANE Select)	AHCYL2	Deleterious	63\|37	simple_aae		No				Single base exchange		Normal	Amino acid sequence changed Heterozygous in gnomAD Protein features (might be) affected
ENST00000446544	AHCYL2	Deleterious	78\|22	simple_aae		No				Single base exchange		Normal	Amino acid sequence changed Heterozygous in gnomAD Protein features (might be) affected

MutationT@ster 2025

Variant:

7:129225306C>T_1_ENST00000325006

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Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Heterozygous in gnomAD
Protein features (might be) affected

Model: simple_aae
Tree vote: 63|37 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr7:129225306C>T (GRCh38)

Gene symbol

AHCYL2

Gene constraints

LOEUF: 0.52, LOF (oe): 0.37, misssense (oe): 0.75, synonymous (oe): 1.01 ? (gnomAD)

Ensembl transcript ID

ENST00000325006.8

Genbank transcript ID

NM_015328 (exact from MANE), NM_001393387 (by similarity), NM_001393390 (by similarity)

UniProt / AlphaMissense peptide

SAHH3_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.230C>T
g.277C>T

AA changes

AAE:	A77V	?
Score:	64

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs758474402
gnomAD	homozygous (T/T)	heterozygous	allele carriers
	4	758	762

Protein conservation

Species	Match	AA	Alignment
Human		77	G	S	G	P	A	A	A	L	S	P	A	A	G	K	V	P	Q	A	S	A	M	K	R	S
mutated	not conserved	77	G	S	G	P	A	A	A	L	S	P	A	V	G	K	V	P	Q	A	S	A	M	K	R
Ptroglodytes	all identical	620	G	S	G	P	A	A	A	L	S	P	A	A	G	K	V	P	Q	A	S	A	M	K	R
Mmulatta	all identical	76	G	S	G	P	A	A	A	L	S	P	A	A	G	K	V	P	Q	A	S	A	M	K	R
Fcatus	all identical	114	G	S	G	P	A	A	A	L	S	P	A	A	G	K	V	P	Q	A	S	A	M	K	R
Mmusculus	all identical	79	G	S	G	P	T	A	A	L	S	P	A	A	G	K	V	P	Q	A	S	A	M	K	R
Ggallus	no alignment	n/a
Trubripes	not conserved	706	S	S	-	-	L	G	L	L	T	P	N	P	V	K	M	P	Q	G	S	A	M	K	R
Drerio	no homologue
Dmelanogaster	no alignment	n/a
Celegans	no alignment	n/a
Xtropicalis	not conserved	61	-	N	S	P	I	P	A	L	S	Q	P	I	K	G	A	P	-	A	S	A	M	K	R

Protein features

Start (aa)	End (aa)	Feature
1	184	REGION	lost
2	109	REGION	lost
2	611	CHAIN	lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	1.307	0.51
	2.767	0.574
(flanking)	-0.342	0.079

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

N/A

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

7

Strand

1

Original gDNA sequence snippet

CGCCGCTCTCAGCCCCGCCGCCGGGAAGGTGCCTCAGGCGT

Altered gDNA sequence snippet

CGCCGCTCTCAGCCCCGCCGTCGGGAAGGTGCCTCAGGCGT

Original cDNA sequence snippet

CGCCGCTCTCAGCCCCGCCGCCGGGAAGGTGCCTCAGGCGT

Altered cDNA sequence snippet

CGCCGCTCTCAGCCCCGCCGTCGGGAAGGTGCCTCAGGCGT

Wildtype AA sequence

MSVQVVSAAA AAKVPEVELK DLSPSEAESQ LGLSTAAVGA MAPPAGGGDP EAPAPAAERP
PVPGPGSGPA AALSPAAGKV PQASAMKRSD PHHQHQRHRD GGEALVSPDG TVTEAPRTVK
KQIQFADQKQ EFNKRPTKIG RRSLSRSISQ SSTDSYSSAA SYTDSSDDET SPRDKQQKNS
KGSSDFCVKN IKQAEFGRRE IEIAEQEMPA LMALRKRAQG EKPLAGAKIV GCTHITAQTA
VLMETLGALG AQCRWAACNI YSTLNEVAAA LAESGFPVFA WKGESEDDFW WCIDRCVNVE
GWQPNMILDD GGDLTHWIYK KYPNMFKKIK GIVEESVTGV HRLYQLSKAG KLCVPAMNVN
DSVTKQKFDN LYCCRESILD GLKRTTDMMF GGKQVVVCGY GEVGKGCCAA LKAMGSIVYV
TEIDPICALQ ACMDGFRLVK LNEVIRQVDI VITCTGNKNV VTREHLDRMK NSCIVCNMGH
SNTEIDVASL RTPELTWERV RSQVDHVIWP DGKRIVLLAE GRLLNLSCST VPTFVLSITA
TTQALALIEL YNAPEGRYKQ DVYLLPKKMD EYVASLHLPT FDAHLTELTD EQAKYLGLNK
NGPFKPNYYR Y*

Mutated AA sequence

MSVQVVSAAA AAKVPEVELK DLSPSEAESQ LGLSTAAVGA MAPPAGGGDP EAPAPAAERP
PVPGPGSGPA AALSPAVGKV PQASAMKRSD PHHQHQRHRD GGEALVSPDG TVTEAPRTVK
KQIQFADQKQ EFNKRPTKIG RRSLSRSISQ SSTDSYSSAA SYTDSSDDET SPRDKQQKNS
KGSSDFCVKN IKQAEFGRRE IEIAEQEMPA LMALRKRAQG EKPLAGAKIV GCTHITAQTA
VLMETLGALG AQCRWAACNI YSTLNEVAAA LAESGFPVFA WKGESEDDFW WCIDRCVNVE
GWQPNMILDD GGDLTHWIYK KYPNMFKKIK GIVEESVTGV HRLYQLSKAG KLCVPAMNVN
DSVTKQKFDN LYCCRESILD GLKRTTDMMF GGKQVVVCGY GEVGKGCCAA LKAMGSIVYV
TEIDPICALQ ACMDGFRLVK LNEVIRQVDI VITCTGNKNV VTREHLDRMK NSCIVCNMGH
SNTEIDVASL RTPELTWERV RSQVDHVIWP DGKRIVLLAE GRLLNLSCST VPTFVLSITA
TTQALALIEL YNAPEGRYKQ DVYLLPKKMD EYVASLHLPT FDAHLTELTD EQAKYLGLNK
NGPFKPNYYR Y*

Position of stopcodon in wt / mu CDS

1836 / 1836

Position (AA) of stopcodon in wt / mu AA sequence

612 / 612

Position of stopcodon in wt / mu cDNA

1883 / 1883

Position of start ATG in wt / mu cDNA

48 / 48

Last intron/exon boundary

1876

Theoretical NMD boundary in CDS

1778

Length of CDS

1836

Coding sequence (CDS) position

230

cDNA position

277

gDNA position

277

Chromosomal position

129225306

Speed

0.07 s

All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project

Back to summary table

MutationT@ster 2025

Variant:

7:129225306C>T_2_ENST00000446544

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Heterozygous in gnomAD
Protein features (might be) affected

Model: simple_aae
Tree vote: 78|22 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr7:129225306C>T (GRCh38)

Gene symbol

AHCYL2

Gene constraints

LOEUF: 0.50, LOF (oe): 0.36, misssense (oe): 0.76, synonymous (oe): 1.01 ? (gnomAD)

Ensembl transcript ID

ENST00000446544.6

Genbank transcript ID

NM_001130720 (by similarity), NM_001393389 (by similarity)

UniProt / AlphaMissense peptide

SAHH3_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.230C>T
g.277C>T

AA changes

AAE:	A77V	?
Score:	64

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs758474402
gnomAD	homozygous (T/T)	heterozygous	allele carriers
	4	758	762

Protein conservation

Species	Match	AA	Alignment
Human		77	G	S	G	P	A	A	A	L	S	P	A	A	G	K	V	P	Q	A	S	A	M	K	R	S
mutated	not conserved	77	G	S	G	P	A	A	A	L	S	P	A	V	G	K	V	P	Q	A	S	A	M	K	R
Ptroglodytes	no homologue
Mmulatta	no homologue
Fcatus	no homologue
Mmusculus	no homologue
Ggallus	no homologue
Trubripes	no homologue
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	no homologue

Protein features

Start (aa)	End (aa)	Feature
1	184	REGION	lost
2	109	REGION	lost
2	611	CHAIN	lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	1.307	0.51
	2.767	0.574
(flanking)	-0.342	0.079

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

N/A

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

7

Strand

1

Original gDNA sequence snippet

CGCCGCTCTCAGCCCCGCCGCCGGGAAGGTGCCTCAGGCGT

Altered gDNA sequence snippet

CGCCGCTCTCAGCCCCGCCGTCGGGAAGGTGCCTCAGGCGT

Original cDNA sequence snippet

CGCCGCTCTCAGCCCCGCCGCCGGGAAGGTGCCTCAGGCGT

Altered cDNA sequence snippet

CGCCGCTCTCAGCCCCGCCGTCGGGAAGGTGCCTCAGGCGT

Wildtype AA sequence

MSVQVVSAAA AAKVPEVELK DLSPSEAESQ LGLSTAAVGA MAPPAGGGDP EAPAPAAERP
PVPGPGSGPA AALSPAAGKV PQASAMKRSD PHHQHQRHRD GGEALVSPDG TVTEAPRTVK
KIQFADQKQE FNKRPTKIGR RSLSRSISQS STDSYSSAAS YTDSSDDETS PRDKQQKNSK
GSSDFCVKNI KQAEFGRREI EIAEQEMPAL MALRKRAQGE KPLAGAKIVG CTHITAQTAV
LMETLGALGA QCRWAACNIY STLNEVAAAL AESGFPVFAW KGESEDDFWW CIDRCVNVEG
WQPNMILDDG GDLTHWIYKK YPNMFKKIKG IVEESVTGVH RLYQLSKAGK LCVPAMNVND
SVTKQKFDNL YCCRESILDG LKRTTDMMFG GKQVVVCGYG EVGKGCCAAL KAMGSIVYVT
EIDPICALQA CMDGFRLVKL NEVIRQVDIV ITCTGNKNVV TREHLDRMKN SCIVCNMGHS
NTEIDVASLR TPELTWERVR SQVDHVIWPD GKRIVLLAEG RLLNLSCSTV PTFVLSITAT
TQALALIELY NAPEGRYKQD VYLLPKKMDE YVASLHLPTF DAHLTELTDE QAKYLGLNKN
GPFKPNYYRY *

Mutated AA sequence

MSVQVVSAAA AAKVPEVELK DLSPSEAESQ LGLSTAAVGA MAPPAGGGDP EAPAPAAERP
PVPGPGSGPA AALSPAVGKV PQASAMKRSD PHHQHQRHRD GGEALVSPDG TVTEAPRTVK
KIQFADQKQE FNKRPTKIGR RSLSRSISQS STDSYSSAAS YTDSSDDETS PRDKQQKNSK
GSSDFCVKNI KQAEFGRREI EIAEQEMPAL MALRKRAQGE KPLAGAKIVG CTHITAQTAV
LMETLGALGA QCRWAACNIY STLNEVAAAL AESGFPVFAW KGESEDDFWW CIDRCVNVEG
WQPNMILDDG GDLTHWIYKK YPNMFKKIKG IVEESVTGVH RLYQLSKAGK LCVPAMNVND
SVTKQKFDNL YCCRESILDG LKRTTDMMFG GKQVVVCGYG EVGKGCCAAL KAMGSIVYVT
EIDPICALQA CMDGFRLVKL NEVIRQVDIV ITCTGNKNVV TREHLDRMKN SCIVCNMGHS
NTEIDVASLR TPELTWERVR SQVDHVIWPD GKRIVLLAEG RLLNLSCSTV PTFVLSITAT
TQALALIELY NAPEGRYKQD VYLLPKKMDE YVASLHLPTF DAHLTELTDE QAKYLGLNKN
GPFKPNYYRY *

Position of stopcodon in wt / mu CDS

1833 / 1833

Position (AA) of stopcodon in wt / mu AA sequence

611 / 611

Position of stopcodon in wt / mu cDNA

1860 / 1860

Position of start ATG in wt / mu cDNA

28 / 28

Last intron/exon boundary

1853

Theoretical NMD boundary in CDS

1775

Length of CDS

1833

Coding sequence (CDS) position

230

cDNA position

257

gDNA position

277

Chromosomal position

129225306

Speed

0.06 s

All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project

Back to summary table